The Complete Mitochondrial Genome from Iraqi Meriz Goats and the Maternal Lineage Using Whole Genome Sequencing Data
محورهای موضوعی : Camel
S.I. Mustafa
1
,
J.S. Heslop-Harrison
2
,
T. Schwarzacher
3
1 - Department of Animal Production, College of Agricultural Engineering Science, University of Duhok, Kurdistan Region, Iraq
2 - Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
3 - Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
کلید واژه: genetic diversity, phylogeny, Next generation sequencing, capra, mitogenome copy number,
چکیده مقاله :
Meriz goat is a native goat breed found along the northern boundary of the Iraqi Kurdistan region near the center of species diversity and domestication. This economically important breed is distinguished by its production of fine hair, high persistence, and ability to thrive in harsh environmental conditions. Although the phenotype and productive traits of the Meriz goat have been described, the complete mitochondrial genome, maternal lineage, and genetic diversity of the breed have yet to be identified. Therefore, the whole genome sequencing data and bioinformatics analysis were used to assemble the complete mitochondrial genome, generate a maternal phylogeny, and identify some mitogenomic diversity features of Meriz goats Meriz goat is a native goat breed found along the northern boundary of the Iraqi Kurdistan region near the center of species diversity and domestication. This economically important breed is distinguished by its production of fine hair, high persistence, and ability to thrive in harsh environmental conditions. Although the phenotype and productive traits of the Meriz goat have been described, the complete mitochondrial genome, maternal lineage, and genetic diversity of the breed have yet to be identified. Therefore, the whole genome sequencing data and bioinformatics analysis were used to assemble the complete mitochondrial genome, generate a maternal phylogeny, and identify some mitogenomic diversity features of Meriz goats from the Iraqi Kurdistan region. The complete mitochondrial genome of the two individuals was assembled with lengths of 16641 and 16639 bp, respectively (MH165338 and MH165339). The mitogenome comprises13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) genes and one non-coding control region. In addition, our data revealed that the mitogenome copy number is greater in female goats than in males. Integration into a phylogenetic tree with other goat breeds showed that Meriz goats belong to the most predominant maternal haplogroup A (HPGA). Furthermore, nucleotide diversity and mitogenomic analysis indicated that Meriz goats have a high level of mitogenomic similarity to Chinese Cashmere goats and Turkish Angora goats within the same maternal lineage. The molecular data reported here provide useful insights into the evolutionary relationships and mitogenomic diversity of domestic and wild goats from the center of diversity of animal species in the Middle East.
Achilli A., BonFigurelio S., Olivieri A., Malusa A., Pala M., Kashani B.H., Perego U.A., Ajmone-Marsan P., Liotta L., Semino O. and Bandelt H.J. (2009). The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PloS One. 4, e5753.
Al-Araimi N.A., Al-Atiyat R.M., Gaafar O.M., Vasconcelos R., Luzuriaga-Neira A., Eisa M.O., Amir N., Benaissa M.H., Alfaris A.A., Aljumaah R.S. and Elnakhla S.M. (2017). Maternal genetic diversity and phylogeography of native Arabian goats. Livest. Sci. 206, 88-94.
Alkass J.E. and Juma K.H. (2005). Small ruminant breeds of Iraq. Pp. 63-101 in Characterization of Small Ruminant Breeds in West Asia and North Africa. L. Iniguez, Ed. International Center for Agriculture Research in the Dry Areas, West Asia. Aleppo, Syria.
Amills M., Capote J. and Tosser‐Klopp G. (2017). Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces. Anim. Genet. 48, 631-644.
Colli L., Lancioni H., Cardinali I., Olivieri A., Capodiferro M.R., Pellecchia M., Rzepus M., Zamani W., Naderi S., Gandini F. and Vahidi S.M.F. (2015). Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics. 16, 1-12.
Daly K.G., Delser P.M., Mullin V.E., Scheu A., Mattiangeli V., Teasdale M.D., Hare A.J., Burger J., Verdugo M.P., Collins M.J. and Kehati R. (2018). Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science. 361, 85-88.
De A.K., Muthiyan R., George Z., Ponraj P., Malakar D., Kundu A., Sunder J. and Bhattacharya D. (2019). Complete mitochondrial genome of Trinket cattle, a Danish colonial leftover. Mitochondrial DNA Part B. 4, 2053-2054.
Deniskova T., Bakoev N., Dotsev A., Selionova M. and Zinovieva N. (2020). Maternal origins and haplotype diversity of seven Russian goat populations based on the D-loop sequence variability. Animals. 10, 1603-1611.
Diwedi J., Singh A.W., Ahlawat S., Sharma R., Arora R., Sharma H., Raja K.N., Verma N.K. and Tantia M.S. (2020). Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats. Gene. 756, 144910-144919.
FAO (2000). Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.
Ganbold O., Lee S.H., Paek W.K., Munkhbayar M., Seo D., Manjula P., Khujuu T., Purevee E. and Lee J.H. (2020). Mitochondrial DNA variation and phylogeography of native Mongolian goats. Asian-Australasian J. Anim. Sci. 33, 902-911.
Gorkhali N.A., Lin J., Sapkota S., Pokhrel B.R., Ma Y.H. and Han J.L. (2021). Origin and Genetic Diversity of Nepalese Indigenous Goats (Capra hircus). Agric. Sci. Dig. 2021, 5-11.
Guang-Xin E., Yong-Fu H., Narisu N., Hui-Jiang G., Zhong-Quan Z., Cao-De J., Jia-Hua Z., Yue-Hui M., Li-Peng C., Yan Z., Ya-Wang S. and Yong-Ju Z. (2016). A complete mitochondrial genome of Dazu Black goat. Mitochondrial DNA Part A. 27, 3171-3172.
Harley E.H., de Waal M., Murray S. and O’Ryan C. (2016). Comparison of whole mitochondrial genome sequences of northern and southern white rhinoceroses (Ceratotherium simum): the conservation consequences of species definitions. Conserv. Genet. 17, 1285-1291.
Hassanin A., Ropiquet A., Couloux A. and Cruaud C. (2009). Evolution of the mitochondrial genome in mammals living at high altitude: New insights from a study of the tribe Caprini (Bovidae, Antilopinae). J. Mol. Evol. 68, 293-310.
Huang Y., Liu N., Zhao Y., He J., Na R., Zhao Z., Jiang C., Zhang J., Ma Y., Chen L. and Qiu X. (2015). Characteristics of the mitochondrial genome of four native goats in China (Capra hircus). Mitochondrial DNA Part A. 27, 3308-3309.
Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C. and Thierer T. (2012). Geneious basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28, 1647-1649.
Kumar S., Stecher G., Li M., Knyaz C. and Tamura K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547-1549.
Laubenthal L., Hoelker M., Frahm J., Dänicke S., Gerlach K., Südekum K.H., Sauerwein H. and Häussler S. (2016). Mitochondrial DNA copy number and biogenesis in different tissues of early-and late-lactating dairy cows. J. Dairy Sci. 99, 1571-1583.
Li Y.Y., Liu L.X., Sui Z.H., Ma C. and Liu Y.G. (2019). The complete mitochondrial DNA sequence of Mongolian grayling Thymallus brevirostris. Mitochondrial DNA Part B. 4, 1204-1205.
Lippold S., Matzke N.J., Reissmann M. and Hofreiter M. (2011). Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evol. Biol. 11, 1-10.
Liu R., Jin L., Long K., Tang Q., Ma J., Wang X., Zhu L., Jiang A.A., Tang G., Jiang Y. and Li X. (2018). Analysis of mitochondrial DNA sequence and copy number variation across five high-altitude species and their low-altitude relatives. Mitochondrial DNA Part B. 3, 847-851.
Lv F.H., Peng W.F., Yang J., Zhao Y.X., Li W.R., Liu M.J., Ma Y.H., Zhao Q.J., Yang G.L., Wang F. and Li J.Q. (2015). Mitogenomic meta-analysis identifies two phases of migration in the history of eastern Eurasian sheep. Mol. Biol. Evol. 32, 2515-2533.
Ma Y., Su R., Fan Y., Qiao X., Li X., Zhang L. and Li J. (2018). The complete mitochondrial DNA analyses of Inner Mongolia Cashmere goat type of Erlangshan species. Mitochondrial DNA Part B. 3, 44-45.
Mannen H., Yonezawa T., Murata K., Noda A., Kawaguchi F., Sasazaki S., Olivieri A., Achilli A. and Torroni A. (2020). Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds. Sci. Rep. 10, 1-7.
Meadows J.R., Cemal I., Karaca O., Gootwine E. and Kijas J.W. (2007). Five ovine mitochondrial lineages identified from sheep breeds of the near East. Genetics. 175, 1371-1379.
Muhammad Salih Al-Barzinj Y., Asmat Oramari R. and Abdulghany Al-Sanjury R. (2016). Molecular characterization of Iraqi local goat breeds using random amplified polymorphicDNA Marestic goats by large-scale mitochondrial DNA markers. Iranian J. Appl. Anim. Sci. 6, 671-678.
Mustafa S.I., Schwarzacher T. and Heslop-Harrison J.S. (2018). Complete mitogenomes from Kurdistani sheep: Abundant centromeric nuclear copies representing diverse ancestors. Mitochondrial DNA Part A. 29, 1180-1193.
Mustafa S.I. (2021). The complete mitogenome of the Iraqi Awassi sheep breed and the maternal lineage utilizing high throughput sequencing raw reads. J. Bangladesh Agric. Univ. 19, 465-470.
Naderi S., Rezaei H.R., Pompanon F., Blum M.G., Negrini R., Naghash H.R., Balkız Ö., Mashkour M., Gaggiotti O.E., Ajmone-Marsan P. and Kence A. (2008). The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proc. Natl. Acad Sci. 105, 17659-17664.
Naderi S., Rezaei H.R., Taberlet P., Zundel S., Rafat S.A., Naghash H.R., El-Barody M.A., Ertugrul O., Pompanon F. and Econogene C. (2007). Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS One. 2, e1012.
Osman S.A.M., Nishibori M. and Yonezawa T. (2021). Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens. Anim. Biosci. 34, 941-948.
Peng S.M., Lin Q., Jiang G.T., Li Y.H., Dai Q.Z., He X. and Yan H.F. (2018). The complete mitochondrial genome of the Dongan black chicken and its phylogenetic analyses. Mitochondrial DNA Part B. 3, 1127-1128.
Rashidi A., Sheikahmadi M., Rostamzadeh J. and Shrestha J.N.B. (2008). Genetic and phenotypic parameter estimates of body weight at different ages and yearling fleece weight in Markhoz goats. Asian-Australasian J. Anim. Sci. 21, 1395-1403.
Seki Y., Yokohama M., Wada K., Fujita M., Kotani M., Nagura Y., Kanno M., Nomura K., Amano T. and Kikkawa Y. (2011). Expression analysis of the type I keratin protein keratin 33A in goat coat hair. Anim. Sci. J. 82, 773-781.
Seyedabadi H.R., Pahlevan Afshari K. and Abdolmaleki M. (2016). Mitochondrial diversity and phylogenetic structure of Marghoz goat population. Iranian J. Appl. Anim. Sci. 6, 679-684.
Shakyawar D.B., Raja A.S.M., Kumar A., Pareek P.K. and Wani S.A. (2013). Pashmina fibre-production, characteristics and utilization. Indian J. Fibre Textile Res. 38, 207-214.
Srirattana K., McCosker K., Schatz T. and John J.C.S. (2017). Cattle phenotypes can disguise their maternal ancestry. BMC Genetics. 18, 1-11.
Tarekegn G.M., Tesfaye K., Mwai O.A., Djikeng A., Dessie T., Birungi J., Osama S., Zergaw N., Alemu A., Achieng G. and Tutah J. (2018). Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats. Ecol. Evol. 8, 1543-1553.
Tillmar A.O., Dell'Amico B., Welander J. and Holmlund G. (2013). A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures. PLoS One. 8, e83761.
Wang Z., Wang R., Zhang W., Wang Z., Wang P., Liu H., Gao L., Bai K., Meng R., Zhou J. and Zhang Y. (2013). Estimation of genetic parameters for fleece traits in yearling Inner Mongolia Cashmere goats. Small Rumin. Res. 109, 15-21.
Xu Y., Liu J., Jiang E., Xu Y., Ning F., Du Z. and Bai X. (2019). The complete mitochondrial genome of Pallas's cat (Otocolobus manul). Mitochondrial DNA Part B. 4, 658-659.
Yang L., Tan Z., Wang D., Xue L., Guan M.X., Huang T. and Li R. (2014). Species identification through mitochondrial rRNA genetic analysis. Sci. Rep. 4, 1-11.
Zeder M.A. (2008). Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. Proc. Natl. Acad. Sci. 105, 11597-11604.
Zhao Y., Zhao R., Zhao Z., Xu H., Zhao E. and Zhang J. (2014). Genetic diversity and molecular phylogeography of Chinese dom. Biol. Rep. 41, 3695-3704.
